quickslice 1.1

Extract slices from compressed volumetric data

quickslice

A simple python package to compress large volumetric data and dynamically extract slices from the compressed volume.

Usage

Build

quickslice build path/to/directory
quickslice build path/to/directory --size 256 256 256

Slice

quickslice slice file.cct -z 0
quickslice slice file.cct -z 0.5
quickslice slice file.cct -x 0.7
quickslice slice file.cct -y 1

Files

quickslice

quickslice is the main binary file

build.py

build.py takes input of a directory containing slices in alphanumeric order and converts it to a CCT (Compressed Computed Tomography) file of size 128 x 128 x 128

slice.py

slice.py is used to extract a slice from a cct file. The following command shows the xy plane at z = 0 of file.cct

Additional Stuff

The z=0 plane output

More examples

More examples and commands with options can be found in examples

CCT File format

Compressed Computed Tomography Files

CCT files represent GBs of Tomographic Datasets in a single compressed file. The file size depends on the output size. The default size is 128 x 128 x 128 and the size of the output file is between 7 MB to 12 MB

Note: Refrain from using CCT files for in-detail visualisation. CCT files are built using a super-lossy conversion technique and are meant to be used for a small quick preview of planes extracted from 3d volumes.

Representation:

Line 1: sizeX,sizeY,sizeZ

Line 2 to Line (sizeZ + 1): Z-Slice representation

The following voxels:

[
    [
        [0,0,1],
        [0,0,1],
        [0,1,1],
        [0,1,1],
        [1,1,1]
    ],
    [
        [0,0,1],
        [0,0,1],
        [0,1,1],
        [0,1,1],
        [1,1,1]
    ],
    [
        [0,0,1],
        [0,0,1],		
        [0,1,1],
        [0,1,1],
        [1,1,1]
    ],
    [
        [0,0,1],
        [0,0,1],
        [0,1,1],
        [0,1,1],
        [1,1,1]
    ] 
]

will be represented as

3,5,4

0,0,1,0,0,1,0,1,1,0,1,1,1,1,1

0,0,1,0,0,1,0,1,1,0,1,1,1,1,1

0,0,1,0,0,1,0,1,1,0,1,1,1,1,1

0,0,1,0,0,1,0,1,1,0,1,1,1,1,1

Example

file.cct is a 128 x 128 x 128 grayscale tomographic model